To know and lose
by maraudergirl68448
Summary: Larger summary inside. My version of what I think will happen at the end of City of heavenly fire!
1. Chapter 1

Hello everyone!

This is more an idea I found really interesting and wanted to attempt to write!

It's set at the end of 'City of heavenly fire' (How I think it would end) and it's based on Clary's reactions to her brother's death.

It's a four chapter story!

Here's the backstory to this story…

*Storyinception*

Clary has been kidnapped by her brother and after two months, Jonathan has brought Clary to Idris to start the war with dark shadowhunters and normal shadowhunters.

Prior to this, during those two months, Clary and Jonathan got along. Jonathan was kind to her and didn't keep (Many) secrets from her.

The story picks up from Jonathan's death.!

Hope you enjoy!


	2. Chapter 2

Clary stared down at the now limp and bloody body that was once her brother.

It was just moments before that Jace had stabbed Sebastian in the back, severing the spine and through the heart.

The sight of her brother locking his sight on Clary was haunting. His deep black eyes fixated on her, as though pleading with her to help him.

Two months ago, Clary would have glared at him, possibly laughed that he would want her help.

But over the length of time that she had been 'kidnapped', Clary had gotten to know much more about her brother.

Jace was staring at her now, shocked by her blood curdling scream that escaped her lips as his sword sank into Sebastian's back.

She should have hated Sebastian. She should be grateful that he was dead. She should be spitting on his body and walking away, knowing she had closure.

But all she felt was anger, not at her brother, but at Jace, her mother and everyone else involved in her brother's death.

She saw Jace walk towards her, his arms outstretched to embrace her. After all, he hadn't seen her in a little less than two months, only knowing she was with her brother.

As soon as Jace stood in front of her, beginning to fold her into his arms, she snapped out of her comatose state and was finally able to move.

She used all of her strength to push Jace away. "Leave me alone!" She growled, using a voice that sounded foreign to her. she never heard herself sound so…angry! Her voice was terrifying, even to her.

Jace stumbled from her push, his expression a mixture of shock, hurt, confusion, anger and…fear?

"Clary…" Whatever he was about to say, died on his lips. He went to attempt to embrace her once more, but Clary pushed past him.

She stumbled to the body of her brother. She kneeled down beside his body. His eyes were still staring at where she was when he died. His eyes never left her until now, not that he could move them.

They were once again in Idris. In a wide and beautiful clearing to be exact. The scenery was beautiful, which made Clary angrier.

Her brother was a monster, yes…but he was like a puppet that was being controlled.

All his life, their father had controlled him. Their father gave him the demon blood before he was born and he was raised with brutal force! What sane person could go through all that and come out an angel?

Valentine had brainwashed her brother, making him see only views that valentine saw. It was incredible (Yet tragic) that Sebastian had been able to change any views he had built into him.

Clary collapsed on her brother, her face buried in his chest. She wanted to hear the steady beating of a heart, but it was silent. She was aware of many eyes watching her, but she didn't care.

This was her brother and she was going to grieve. He deserved that at least…

Clary felt her tears fall from her eyes and land on her brothers shirt, making it wet. She couldn't, wouldn't stop the tears.

It was incredible that in two months, her attitude towards the person she held the most hatred and murderous rage had changed.

She had seen a completely different side to him. She saw the side of him that was hidden by years of abuse and anger. The side that had only brotherly affections. Of course his demon side slipped up and his intentions became more sick and sinister, but she was able to fend him off.

Clary looked into her brothers now dead and distant black eyes. she could see glimpses of green cracks in his irises. She wondered if he would have had green eyes if it weren't for Valentine.

She reached up a hand and closed his eyes, making it seem like he was sleeping…

Something white in the inside of Jonathan's leather jacket that he used for hunting caught her attention. Upon further inspection, she saw it was a thick envelope with her name written neatly on it.

She took it out of his jacket, but before she could open the envelope, she felt arms wrap around her waist and hoist her back, away from her brother.

She struggled against the hold, noticing the familiar scent that reminded her of sunshine. She knew it was Jace.

She had the envelope in her grasp, but she didn't want to go. She wanted to stay by her brother's side.

She kicked, swore and wiggled, but it was useless. Jace's arms felt like iron bars, securing her to him.

Clary looked back at her brothers prone body until a crowd of shadowhunters circled around.

Many turned around at the sound of her heart wrenching and angry scream, telling them to leave her brother alone.


	3. Chapter 3

**Hello everyone! Sorry for the wait! **

**Thank you all for the support for this story! Means alot!**

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Clary was lying on a bed in one of the many guest rooms of the institute.

After Jace dragged her away from the scene of her dead brother and through a portal Magnus made, she had thrown a fit using language she never used before.

Jace had tried to get Magnus to enter her mind to change whatever her brother had done, leading Clary to punch Jace unexpectantly. She would admit she was proud of herself that she had caught Jace off guard.

He fell to the floor, holding his jaw, where she had hit him, and stared at her in shock and hurt etched all over his face.

Clary remembered her exact words that she had spat at him. It had only been a few short hours ago.

"I hate you and will never forgive you!" it came out as low whisper, which made it even more chilling.

Jace's eyes glistened, like tears would begin brimming over, but Clary ran. She ran through the hallways of the institute until she was lost and had entered the closest door which was a guest room.

She jumped on the bed and had cried into the fresh smelling pillow.

She was laying on her back now, tears still streaming down her cheeks but she didn't bother wiping them away. More tears would soon follow, causing her to wipe more away.

The sky outside the window had turned from morning blue to red sunset. Clary realized she hadn't eaten in at least a day, but she didn't feel hungry. She felt sick to her stomach in fact.

She had waited for the others to come find her, but her stunt with Jace must have convinced them to stay away from her.

Clary switched her gaze from the plain white ceiling, to the white and bulky envelope in her grasp.

She was dying to open it and read its contents, but was nervous for the same reason.

Taking a deep breath, Clary sat up and crossed her legs before ripping open the end of the envelope.

She spilled its contents onto the bed. Three thick pieces of ivory coloured pages fell onto the bed, her brothers neat and cursive hand writing sprawled across the pages.

There was two photographs. They both contained Clary and Jonathan. One was of them in Barcelona at the adventure park 'Portaventura'. Clary had begged for them to do something Mundane, and was excited to go on the tallest roller coaster in Europe. The picture showed Clary and her brother taking a picturein front of a saloon, smiling at the camera.

The other picture was of Clary and Jonathan swimming with dolphins in Portugal. Clary laughed at the memory of Jonathan becoming mad when all the dolphins swam away from him. Clary had made him copy her movements as he was being too quick and straight forward that he scared off the mammals. The picture showed them wearing life jackets, again smiling at the camera as they both had an arm around a dolphin.

Clary looked at one of the last two items that fell out of the envelope. It was Jonathan's bracelet.

Acheronta Movebo.

Clary immediately pulled it onto her wrist. She had to circle it around her wrist twice so it wouldn't fall off. She didn't know why she felt the need to wear it, maybe because it was a piece of her brother…

The last item she hadn't looked at now caught her attention.

It was a key.

Not an ordinary key, the part that looked like it should fit into a door was odd and beautiful. It had intricate metal strands that entwined and looked like ivy the decorated the outside of old buildings.

One end was a mass of designs while the other, the swirls of design created the image of an M.

Clary decided to read the letter before trying to figure out the meaning of the strange key. Picking up the seemingly expensive paper, Clary began to read.

_To my dear sweet sister, Clarissa._

_If you are reading this, I presume the worst has happened and I was killed, hopefully not at your hand._

_I wrote this letter for you, so that you would always have some of my final thoughts with you._

_Over the last two months, you may not believe me, but they were two of the best months of my life._

_As you know, our father wasn't the most...compassionate and our mother abandoned me because she was afraid. You listened to me and I could see the understanding in your eyes._

_You wouldn't understand the feeling of another person's acceptance towards you when all your life you've been a weapon being developed._

_I owe you so much for showing me honest compassion._

_This is one of the reasons that I am writing this letter._

_Now that I'm gone, as the last Morgenstern you receive all assets I had inherited. This includes Morgenstern Manor, the second dimensional apartment we stayed in over the previous two months, everything in both estates and last of all, the infernal cup._

_I know you disagreed with my use of it, but there may be a chance you can use it to your advantage and use it to change the unfairness of the clave, maybe even make the shadow world better._

_I forgot to mention, the shadowhunters that are already turned, are ordered by me to be loyal to you if anything happened to me. Use them well._

_I'm hoping you are the one to read this letter, as I want the choice of what happens to the cup and everything it's done, to be up to you._

_You will find the cup in Morgenstern Manor. Use the specialized key. You'll know how and when to use it._

_I was planning for you to create a rune to find it, so no idiots from the clave could lay their hands on it. It's hidden very well if I may say so myself._

_Aside from the talk of inheritance, I wanted to write this letter so I could apologize. I know I could write a book on everything I should be apologizing for, but a letter will have to do for now._

_I want to apologize for taking Jace away from you in the first place, instead of you. I'm sure you would have refused to come with me willingly, but we won't know that now, will we?_

_I want to apologize for acting on feelings that disgusted you. I won't lie and say those feelings are gone, but I do apologize for making you uncomfortable._

_I want to apologize for causing you so much pain and grief. You didn't deserve it and yet you were caught in the middle of it all._

_I especially wanted to apologize for only getting to know you in a short amount of time. I wish we could have had much more time together._

_I must admit that I knew of you when our father learned of your existence. Months before we ever met. I knew who you were and what we were to each other._

_If it wasn't for our father, I would have dropped everything, just to make up for lost time._

_Of course I was furious at first when I learned that women left me behind because she hated me and went to raise you, but I started to think after a while of what it meant._

_I thought about how there was someone in the world like me. Someone who could understand me and someone who could show me everything I was deprived of all my life._

_Affection._

_Compassion._

_Faith._

_Trust._

_Someone that would look for me for help._

_Love._

_Would you believe that you're the first person to make me genuinely smile? Even laugh?_

_I may not have shown it, but you are the most important thing to me. I would quite literally move heaven and raise hell just to make you smile. You may think that's an exaggeration, but it's the truth._

_I hope you can find it in your heart to forgive me for all of my misdeeds. If I could travel through time, I would change many events just to get more time with my little sister._

_I hope that one day, we can meet again. Maybe not in heaven or hell, but if there was a chance to have be reborn, I would search the earth for you and spend every moment trying to learn more about you and show you how much you mean to me…_

_I know this letter sounds like the work of a mad man, whose to say what's normal?...but as I've already said, this letter is for you to know of some of my final thoughts and to tie up loose threads._

_So, dear sister. This is where I end this letter._

_Burn it_

_Keep it._

_Keep it under lock and key._

_It is up to you, I just hope you read it and understood its contents._

_I will always love you, as a sister and more. I hope whatever choices you make, work in your favor._

_You're brave, intelligent, compassionate and so much more. Never change for anyone or anything._

_Love always, as I will love you._

_You brother, Jonathan Morgenstern._

More tears streamed down her face as she finished the letter.

She knew what her next step would be.


	4. Chapter 4

**Hello everyone! Sorry for the wait! I wrote this chapter out so many times and couldn't get it right! I finally decided on a version I was happy with! I hope you all enjoy! :) Thank you all for your support! **

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Clary quickly stashed all the contents of the envelope in her pockets, including the letter. She still had the bracelet on her wrist and the leather gear she had been wearing in Idris was still together as she hadn't been fighting much.

She needed to get to the weapons room to get a few weapons and a stele. All she had in Idris was a seraph blade which she had dropped when she watched her brother's body crumple to the ground. She then remembered she had a Morgenstern embalmed dagger in her right boot.

She walked over to the door of the room, putting the right side of her ear against the wood. She listened for the sound of footsteps or of people talking. She breathed a sigh of relief when a no sound could be heard.

She wrenched open the door, planning to run straight to the weapons room, but stopped as a golden figure stood across the hallway from her.

Jace was leaning against the wall, his arms crossed and his eyes staring straight at her. He still wore the hunting gear that he had been wearing in Idris.

Staring back at him, Clary noticed he had bags under his eyes, his face looked more sullen and he looked like he lost some weight.

She briefly wondered if he had neglected his appetite and sleep patterns. He looked like he hadn't eaten or slept in weeks! Had she been the cause of it all?

The thought added to her already anger filled mind.

She was furious with him for murdering her brother, but the fact he was putting his health at risk because of her which could lead him to becoming sick and getting himself killed causing his whole family to grieve as they already lost a son/brother.

That train of thought made her livid.

"What are you doing here." She hissed between her teeth which she was forcing not to grind against her teeth.

Jace looked shocked and taken aback, but he quickly composed himself. "I was looking for you and then I was awaiting for you to leave that room so we could talk."

Clary could swear she felt her eye twitch. "You want to talk? Really? Well screw you Jace! How's that for talking?" She crossed her own arms, momentarily forgetting the bracelet.

Jace noticed it straight away. "What has he done to you Clary." He detached himself from the wall and stepped closer to her. "This isn't you. We can help you."

Her whole body was vibrating with angry energy as she tried to keep herself under control. "Jonathan has done nothing to me. But you're right. This isn't me. Two months ago, I would have hidden behind you to protect me because my mother never trained me. I would have been the little weakling that screws everything up. Jonathan trained me in two months. He brought me hunting as well. He didn't think I was something that had to be protected. He thought I was someone who can fight and defend themself."

Jace again looked shocked at her. "Clary, I don't think you're weak. I don't think you screw everything up. Yes you weren't trained, but we were training you!"

Clary rolled her eyes. "Oh please. You think that every time I get involved, everything goes wrong. I bet you blame me for the heavenly fire you have."

"I don't blame you! Why are you acting like a...a..."

"A what, Jace? What am I acting like? Let me guess, I'm acting like a drama queen. Well excuse me for no being full of joy because you killed my brother!"

"I wasn't going to say that! And I had no choice! *Sebastian* killed out of cold blood. He was going to kill everyone living on earth! How can you possibly try to defend that?!"

"His name is not Sebastian! He wasn't going to destroy the earth! And what were you going to say then?"

"Whatever his name was, I'm pretty sure he told me while he was controlling me that he was going to burn the earth to ashes."

"There was a reason he was planning to do that. But answer my first question." she said while narrowing her eyes at the golden boy.

"I would love to hear that explanation." He replied, frowning at her.

"Nice try, answer my question."

"Fine. You're acting like a version of your brother!"

Clary felt her lips pull into a smirk. "And if I am?"

Jace frowned further. "What are you-" His words were cut off into a groan as Clary took him by surprise as she quick as a flash pulled her dagger out of her boot and pushed the blade into his stomach.

He fell to his knees as soon as she pulled out the dagger, clutching his stomach as blood poured from the wound. She watched as he fumbled in his pocket, producing a stele.

He lifted his shirt, but before he could attempt to draw an iratze, Clary kicked the stele from his hand. He gasped as he tried to catch the stele, but only to end up on his side, one hand still clutching his wound.

Clary bent towards him, his still open golden eyes staring into her green ones. He looked like he was trying to say something, but as his eyes began to droop, Clary said her final goodbye to him.

"I'm going to make my brother proud."

His eyes finally closed, Clary could hear yelling coming from one part of the institute. She knew it was Alec without even having to think about it.

She stood up from her crouch, feeling numb. She wasn't sure what to feel. She had stabbed her first love. She wasn't sure what to feel.

Shaking her head, she quickly ran to grab the stele Jace had. Looking back at his body, she noticed he had a two seraph blades and a few other weapons she wasn't sure how to use. She took the seraph blades, considering for a moment leaving.

Why should he live? He killed her brother! How is his life more valuable?

_Because you still and will always love him you idiot._

Silently cursing herself, Clary placed the blades in her belt and retrieved the stele. She drew an iratze on his stomach, above the wound and then drew another rune that would leave him in his unconscious state for a while longer.

The yelling had ceased, but Clary knew it was only a matter of time before everyone in the institute appeared.

Clary began running through the hallways, drawing a rune that would make her invisible. She wasn't sure it worked till she stood to the left of the hallway as Isabelle and Magnus rushed past.

She smirked again as she realised she was able to walk through the hallways without being caught.

She made her way to the weapons room without running into anyone else thankfully. She entered the room that she doubted would ever run out of weapons.

She quickly decided on a few weapons.

She had been practising with a sword with Jonathan for a few days before he tried making her train with a katana. Clary was able to fight better with a Japanese sword, but sadly the institute didn't have any. She decided on the lightest sword she could find. She then equipped herself with three more daggers as well as the Jace blood covered dagger she had put in her boot again.

She decided to bring a bow and a quiver of arrows with her as well. She knew Alec would certainly miss them, but in that moment...she didn't care.

She placed the bow over her head and clipped the quiver onto her belt

. Jonathan had thought her how to use a bow. She had wanted to compare herself to Alec...that wasn't going to happen any time soon.

Knowing she wouldn't be able to leave the institute without running into anyone, and not knowing how long the invisibility rune would last, Clary decided to draw a portal on the door of the weapons room.

As the swirling portal came into view, Clary was about to step into it when she heard the door being banged on.

"Clarissa, are you in there?" Came the voice of Magnus.

She glared in the direction of Magnus. "What if it is?"

"Come out. Whatever is going on, we can talk it out and figure things out."

Clary laughed without humour. "Why do you all think I'm damaged?"

"Darling, you were with your psychotic brother for two months. Jace is unconscious and there is an unknown rune on him. Want to explain that?"

"My brother did nothing to me!" Clary exclaimed when suddenly she noticed the locking rune becoming faint.

Magnus was breaking in!

"Darl-"

"Don't darling me!" Clary hissed as she jumped into the portal as the door banged open.

Clary guessed the portal shattered from the impact of the bang because when she looked back, it was gone.

Clary looked around to where she was. She felt her body slump when she realised she was in Idris. She had planned to come here, but as she remembered the last time she was there, it was one of the last places she wanted to be.

TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI/TMI

After hours of searching through forests, Clary slumped against a tree trunk. She rested her head against her the tree, closing her eyes and welcoming sleep.

Except every sound she heard caused her heart to accelerate and put her on high alert.

She had no idea where Morgenstern Manor was. She didn't even know what part of the forest she was in! She only knew she was in Idris because there were plants that only grown in Idris around her.

Clary had been walking for so long in the dark and she now couldn't take another step and she slowly realised she hadn't eaten in who knows how long. The sun was at its peak, a new day breaking.

Clary streched and just wanted to sleep. But if she slept, that meant she would be vulnerable to any shadowhunter, demon or downworlder that crossed her path.

She would sleep when she reached Morgenstern Manor. Hopefully she would find it soon.

Another realization hit her as she remembered she could just make a rune that lead her to her destination. She had used her runes before to keep her warm, to make her untraceable and for her to be silent.

How had this not crossed her mind before?

Closing her eyes again, this time in concentration, Clary focused on a rune to help her find a place she had never been. Of course nothing happened.

She wished her brother was there. He could at least show her the way. She was probably walking further from it.  
Another idea came to mind.

She had never been to Morgenstern Manor and wasn't familiar with the forest that covered most of Idris. But Jonathan did. He had led her to Fairchild Manor. He had grown up in Morgenstern Manor. He would have familiarised himself with the forest.

She could create a rune that gave her *his* memories.

She hoped it worked as she closed her eyes in concentration. Not to long before an image appeared of a rune. It was of a triangle with many slashes through it.

She took out Jace's stele from her pocket and placed it against the base of her wrist. Taking a deep breath, she copied the rune onto her skin.

She kept Jonathan in her mind, hoping it worked. As soon as the rune was finished, Clary grabbed her head in pain and let out a strangled cry. It was like someone was pounding her head against a metal wall of spikes. She closed her eyes, wanting to welcome the safety of unconsciousness.

Swirls of colour appeared behind her eyelids. Confused and thinking her rune was a failure, Clary tried to slash her wrist with the stele so she could stop whatever the rune was doing when a scene appeared in her mind.

_The ground is cold. Really cold. _

_I'm in a pool of dark blood that looks black. My back is in agony. I can't move without whimpering._

_Father is somewhere behind me. I can practically feel him smirking at me in satisfaction that he rendered me unable to move, although he wont admit it as he will rant that I am too weak._

_I wouldn't speak like that if I were him. If I let my dark side take over without controlling it, there's nothing that whip of his can do._

_He tells me the whip is to teach me how to control my demon side better. The side he has cursed me with by turning his first-born son into an experiment. _

_I've seen him with the other boy. The golden boy._

_He treats that Jonathan far better than me. He treats another's son far better than his own. Why? Why can't he treat me like that?_

_Why does he treat me like the monster and the other boy like a precious angel?_

_Well father. If the other Jonathan means more to you than your own son...I hope you won't treat me any less when I turn him into a monster as well._

Clary fell forward. It was a memory! It wasn't her memory though. It must be Jonathan's. The image of being on a floor surrounded by her brothers blood would be burned into her brain for the rest of her life.

She felt relief when she realised the pain in her head had ceased. But the rune was still defined on her wrist. She wasn't sure how long it took to fade, but Clary knew she would have to make the most of it while she still had it.

She closed her eyes again, trying to think of Morgenstern Manor. Almost instantly she got an answer.

_Father wants me to go into the forest and uproot a perimeter of ten yards worth of trees. While he's going to spend the day with the other Jonathan as it's his birthday._

_My birthday on the other hand involved me getting to train with new weapons. What is father doing to me? He's taken everything away from me. What do I have left?_

_No emotions, no humanity and no morals. _

_I'm leaving the Manor into the warmth of the summer day. Looking back at the Manor, Jonathan felt much distaste for it. On the outside it was architectural masterpiece._

_ It was a four-story mansion with beige bricks brought from Italy. There was vines crawling up the walls, flowers doting the ivy in places. All the windows were big enough to allow a person to walk through without having to crouch. there was a staircase that led from the ground to the second floor on the outside which led to balcony doors that opened onto the second floor landing. The roof was a steep black shingled slope. A tower sat atop the roof, which father used to trap Jonathan for punishments as there was one way in and out. There were no windows to climb out of and no secret passages.  
_

_The Manor once housed dinner parties for the best of shadowhunters, but since father is supposedly dead...not many would go to the Manor of an evil dead man. _

_I turned around, facing the forest and walking through it. Not sure where the best place to make a clearing of ten yards of trees would be, I decided to go to Fairchild Manor._

_Not like anyone visited his sad excuse of a mother's home_

_It took two hours to reach the remains of the burned down Manor. What he would give to see it a flame. To see his mothers anguish as she saw her own parents were dead. To see the place she called home resembling ash._

_He had only been to the burned remains of the Manor three of four times with his father. His father brought him to remind him that his own mother had forsaken him._

_He had never been there by himself._

Clary snapped open her eyes. She had been to Fairchild Manor with Jonathan who was Sebastian at the time. She could use a locating rune on Fairchild Manor and use Jonathan's memories to find Morgenstern Manor!

Her head was slightly dizzy. It wasn't comfortable having your dead brothers memories take over your head. She was seeing his memory as him. She had no conscious thoughts herself while in her brothers memory.

Clary shook her head as she heaved herself into a standing position. She still had the stele in her grip which had been tightly held as it imprinted its design into her skin.

She quickly drew the locating rune on her arm, hoping it worked. When she felt a tug leading her in a specific way,, Clary felt a smile tug at her lips.

She didn't know what she would do when she reached Morgenstern Manor or get the Infernal cup. she did know she would make her brother proud and make sure he didn't die in vain.

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**Clary turning evil? :O**

**I know I said this would be a four chapter story, but I'm kind of bringing the story in a different direction to where I intended! What would you al say about me making this story longer?**

**I was thinking about (after I receiving the idea from a reviewer) Clary bringing Jonathan back. Or should I stick to him being dead and Clary turning evil by herself?**

**Or should I attempt to finish this story off in the next chapter? **

**Please let me know! :)**

**Till next time ~Maraudergirl68448**


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